diff cuffquant_wrapper.xml @ 3:6dc45faebc1d draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5

--- a/cuffquant_wrapper.xml	Tue Feb 07 18:40:42 2017 -0500
+++ b/cuffquant_wrapper.xml	Sun Feb 19 12:09:41 2017 -0500
@@ -1,13 +1,12 @@
-<tool id="cuffquant" name="Cuffquant" version="@VERSION@.0">
+<tool id="cuffquant" name="Cuffquant" version="@VERSION@.1">
     <!-- Wrapper supports Cuffdiff versions 2.2.1 -->
     <description>Precompute gene expression levels</description>
     <macros>
       <import>cuff_macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <expand macro="stdio" />
     <version_command>cuffquant 2>&amp;1 | head -n 1</version_command>
-    <command>
+    <command detect_errors="aggressive"><![CDATA[
         cuffquant
             --no-update-check
             --num-threads=\${GALAXY_SLOTS:-4}
@@ -51,7 +50,7 @@
             '$gtf_input'
             #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] )
             '$samplestring'
-    </command>
+    ]]></command>
     <inputs>
         <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts"
             help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/>